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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ), 'gf_id' => 'HOM05D001496', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001496' ), 'data_identifier' => 'HOM05D001496', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001496', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '423', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09110' => 'bna', 'A02p38720' => 'bna', 'A05p00200' => 'bna', 'A06p41170' => 'bna', 'A07p21830' => 'bna', 'A09p05390' => 'bna', 'Aa31LG11G9440' => 'aar', 'Aa31LG1G29100' => 'aar', 'Aa31sc27G130' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2558' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.922' => 'aag', 'Actinidia00026' => 'ach', 'Actinidia02729' => 'ach', 'Actinidia24335' => 'ach', 'Actinidia24834' => 'ach', 'Ah.16g101380' => 'amhyb', 'Ah.16g104090' => 'amhyb', 'AL4G47330' => 'aly', 'AL5G34870' => 'aly', 'AL6G39320' => 'aly', 'Aqoxy2G02984' => 'aox', 'Aqoxy2G02988' => 'aox', 'Aqoxy5G00717' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4R66UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4F8D3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RVL32D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XX77X8' => 'arhy', 'AT2G47760' => 'ath', 'AT3G53890' => 'ath', 'AT5G27700' => 'ath', 'ATR0582G253' => 'atr', 'ATR0796G178' => 'atr', 'ATR0796G343' => 'atr', 'Atru.chr2.25' => 'acertr', 'Atru.chr2.3708' => 'acertr', 'Atru.chr4.2833' => 'acertr', 'Atru.chr5.1181' => 'acertr', 'AUR62012333' => 'cqu', 'AUR62022975' => 'cqu', 'AUR62023205' => 'cqu', 'AUR62023251' => 'cqu', 'BcaB01g00230' => 'bca', 'BcaB02g07763' => 'bca', 'BcaB02g08503' => 'bca', 'BcaB02g08748' => 'bca', 'BcaB04g19440' => 'bca', 'BcaB04g19681' => 'bca', 'BcaB07g34198' => 'bca', 'BcaC01g05022' => 'bca', 'BcaC02g12544' => 'bca', 'BcaC03g17797' => 'bca', 'BcaC03g17798' => 'bca', 'BcaC07g39744' => 'bca', 'BcaC08g44650' => 'bca', 'BolC2t11890H' => 'bol', 'BolC3t15455H' => 'bol', 'BolC8t50517H' => 'bol', 'BraA02t08849Z' => 'bra', 'BraA03t11820Z' => 'bra', 'BraA05t19016Z' => 'bra', 'BraA06t26660Z' => 'bra', 'BraA06t27040Z' => 'bra', 'BraA07t29865Z' => 'bra', 'BraA09t36177Z' => 'bra', 'C02p58240' => 'bna', 'C03p31050' => 'bna', 'C04p00120' => 'bna', 'C06p21660' => 'bna', 'CAN.G129.26' => 'can', 'CAN.G1323.1' => 'can', 'CAN.G1538.7' => 'can', 'CAN.G339.32' => 'can', 'CAN.G788.2' => 'can', 'CANSAT11G0303' => 'cansat', 'CANSAT21G0078' => 'cansat', 'CANSAT25G1124' => 'cansat', 'CARHR143130' => 'chi', 'CARHR148820' => 'chi', 'CARHR163790' => 'chi', 'CARHR186220' => 'chi', 'Carub.0004s3047' => 'cru', 'Carub.0005s0586' => 'cru', 'Carub.0005s2047' => 'cru', 'Carub.0006s2488' => 'cru', 'Ca_01938_v3' => 'car', 'Ca_07875_v3' => 'car', 'Ca_09147_v3' => 'car', 'Ca_17726_v3' => 'car', 'CBR_g23454' => 'cbr', 'CBR_g28482' => 'cbr', 'CBR_g8281' => 'cbr', 'Cc01_g20650' => 'ccan', 'Cc03_g01970' => 'ccan', 'CDE01G0133' => 'cde', 'CDE02G4632' => 'cde', 'CDE04G1871' => 'cde', 'Cfa005950' => 'cfa', 'Cfa017109' => 'cfa', 'Ciclev10003001m.g' => 'ccl', 'Ciclev10003006m.g' => 'ccl', 'Ciclev10020260m.g' => 'ccl', 'CiPaw.01G042500' => 'cil', 'CiPaw.01G148900' => 'cil', 'CiPaw.02G083100' => 'cil', 'CiPaw.03G111500' => 'cil', 'CiPaw.04G150800' => 'cil', 'CiPaw.07G066100' => 'cil', 'CiPaw.07G093300' => 'cil', 'CiPaw.07G106500' => 'cil', 'CiPaw.11G085000' => 'cil', 'CiPaw.12G013600' => 'cil', 'CiPaw.15G182100' => 'cil', 'CiPaw.16G069500' => 'cil', 'ClCG00G002600' => 'cla', 'ClCG05G006070' => 'cla', 'ClCG06G005150' => 'cla', 'ClCG09G006040' => 'cla', 'COL.COLO4_05649' => 'col', 'COL.COLO4_10513' => 'col', 'COL.COLO4_15168' => 'col', 'COL.COLO4_23374' => 'col', 'Cpa.g.sc48.90' => 'cpa', 'Cpa.g.sc9.209' => 'cpa', 'Cpa.g.sc9.39' => 'cpa', 'Cre03.g203450' => 'cre', 'CsaV3_3G014610' => 'csa', 'CsaV3_6G017200' => 'csa', 'CsaV3_7G029100' => 'csa', 'CSS0006721' => 'camsi', 'CSS0023433' => 'camsi', 'CSS0033035' => 'camsi', 'CSS0044391' => 'camsi', 'CSS0045492' => 'camsi', 'DCAR_002814' => 'dca', 'DCAR_027247' => 'dca', 'DCAR_030530' => 'dca', 'Dinv19717' => 'din', 'Dinv19719' => 'din', 'Dinv30804' => 'din', 'Duzib128G1213' => 'dzi', 'Duzib133G1333' => 'dzi', 'Duzib177G1135' => 'dzi', 'ECA236G2352' => 'eca', 'ECA247G0314' => 'eca', 'ECA247G2623' => 'eca', 'ECA248G3024' => 'eca', 'EL10Ac2g04497' => 'bvu', 'EL10Ac4g09720' => 'bvu', 'Eucgr.B01917' => 'egr', 'Eucgr.H01160' => 'egr', 'Eucgr.H04516' => 'egr', 'FAN05G0421' => 'fan', 'FAN12G4046' => 'fan', 'FAN14G5180' => 'fan', 'FAN15G0073' => 'fan', 'FAN15G3342' => 'fan', 'FAN17G2082' => 'fan', 'FAN20G0671' => 'fan', 'FAN24G2787' => 'fan', 'FAN27G2092' => 'fan', 'FvH4_2g25370' => 'fve', 'FvH4_4g17990' => 'fve', 'FvH4_6g28030' => 'fve', 'Glyma.03G213200' => 'gma', 'Glyma.07G247600' => 'gma', 'Glyma.09G045000' => 'gma', 'Glyma.15G147700' => 'gma', 'Glyma.19G210000' => 'gma', 'Gohir.A01G111300' => 'ghi', 'Gohir.A01G167500' => 'ghi', 'Gohir.A02G071100' => 'ghi', 'Gohir.A05G239300' => 'ghi', 'Gohir.A07G160700' => 'ghi', 'Gohir.A11G267500' => 'ghi', 'Gohir.A11G294900' => 'ghi', 'Gohir.A12G010700' => 'ghi', 'Gohir.A12G153600' => 'ghi', 'Gohir.A13G108900' => 'ghi', 'Gohir.A13G174300' => 'ghi', 'Gohir.D11G277500' => 'ghi', 'Gohir.D11G309600' => 'ghi', 'Gohir.D12G011100' => 'ghi', 'Gohir.D13G111800' => 'ghi', 'Gohir.D13G180000' => 'ghi', 'Gorai.007G299700' => 'gra', 'Gorai.007G341600' => 'gra', 'Gorai.008G011100' => 'gra', 'Gorai.013G125500' => 'gra', 'Gorai.013G205400' => 'gra', 'GSVIVG01017756001' => 'vvi', 'GSVIVG01027976001' => 'vvi', 'GSVIVG01031151001' => 'vvi', 'HanXRQChr02g0036541' => 'han', 'HanXRQChr02g0043911' => 'han', 'HanXRQChr03g0069931' => 'han', 'HanXRQChr04g0118701' => 'han', 'HanXRQChr05g0138141' => 'han', 'HanXRQChr05g0142891' => 'han', 'HanXRQChr06g0179501' => 'han', 'HanXRQChr06g0182621' => 'han', 'HanXRQChr10g0290691' => 'han', 'HanXRQChr11g0338801' => 'han', 'HanXRQChr11g0339541' => 'han', 'HanXRQChr12g0382731' => 'han', 'HanXRQChr13g0423191' => 'han', 'HanXRQChr14g0435651' => 'han', 'HanXRQChr14g0450021' => 'han', 'HanXRQChr16g0527821' => 'han', 'Haze_01206' => 'cav', 'Haze_01207' => 'cav', 'Haze_04897' => 'cav', 'Haze_26233' => 'cav', 'Haze_26252' => 'cav', 'Hma1.2p1_0078F.1_g040580' => 'hma', 'Hma1.2p1_0209F.1_g088590' => 'hma', 'Hma1.2p1_0209F.1_g088600' => 'hma', 'Hma1.2p1_0209F.1_g088640' => 'hma', 'Hma1.2p1_1212F.1_g267300' => 'hma', 'Hma1.2p1_1292F.1_g273660' => 'hma', 'HPP92_009700' => 'vpl', 'HPP92_015922' => 'vpl', 'HPP92_015933' => 'vpl', 'HPP92_016892' => 'vpl', 'HPP92_016896' => 'vpl', 'Hund13514' => 'sun', 'Hund15854' => 'sun', 'Hund16196' => 'sun', 'Lalb_Chr04g0259801' => 'lal', 'Lalb_Chr04g0259811' => 'lal', 'Lalb_Chr06g0165031' => 'lal', 'Lalb_Chr15g0083511' => 'lal', 'Lalb_Chr18g0051701' => 'lal', 'Lalb_Chr20g0114541' => 'lal', 'Lj1g0019023' => 'lja', 'Lj2C1190T13' => 'lonja', 'Lj4g0024324' => 'lja', 'Lj6g0007538' => 'lja', 'Lsat_1_v5_gn_1_108700' => 'lsa', 'Lsat_1_v5_gn_1_25420' => 'lsa', 'Lsat_1_v5_gn_5_137300' => 'lsa', 'Lsat_1_v5_gn_5_190521' => 'lsa', 'Lsat_1_v5_gn_9_87701' => 'lsa', 'Manes.05G064100' => 'mes', 'Manes.08G118300' => 'mes', 'Manes.09G169800' => 'mes', 'Mapoly0077s0004' => 'mpo', 'Mapoly0090s0015' => 'mpo', 'MBI14_g09685_MAGBIO' => 'mbi', 'MBI18_g21839_MAGBIO' => 'mbi', 'MBI19_g29226_MAGBIO' => 'mbi', 'MBI19_g29447_MAGBIO' => 'mbi', 'MCO05G420' => 'mco', 'MCO08G143' => 'mco', 'MD03G1285100' => 'mdo', 'MD03G1285200' => 'mdo', 'MD11G1125000' => 'mdo', 'MD11G1304600' => 'mdo', 'MD13G1168900' => 'mdo', 'MD16G1170000' => 'mdo', 'Medtr2g436800' => 'mtr', 'Medtr7g076530' => 'mtr', 'Medtr7g108620' => 'mtr', 'MELO3C006662.2' => 'cme', 'MELO3C016018.2' => 'cme', 'MELO3C021332.2' => 'cme', 'Migut.D00196' => 'egut', 'Migut.D01610' => 'egut', 'Migut.G00165' => 'egut', 'Nitab4.5_0000435g0110' => 'nta', 'Nitab4.5_0000619g0030' => 'nta', 'Nitab4.5_0000836g0050' => 'nta', 'Nitab4.5_0000960g0040' => 'nta', 'Nitab4.5_0001078g0050' => 'nta', 'Nitab4.5_0001326g0160' => 'nta', 'Nitab4.5_0005474g0020' => 'nta', 'Nitab4.5_0006554g0010' => 'nta', 'Nitab4.5_0008499g0010' => 'nta', 'Nn2g14201' => 'nnu', 'Nn3g21438' => 'nnu', 'Nn4g25863' => 'nnu', 'Nn4g25864' => 'nnu', 'Nn7g38144' => 'nnu', 'Oeu002440.1' => 'oeu', 'Oeu010915.1' => 'oeu', 'Oeu017404.1' => 'oeu', 'Oeu043360.1' => 'oeu', 'Oeu048346.1' => 'oeu', 'Os01g0172000' => 'osa', 'Os03g0345200' => 'osa', 'Os03g0667800' => 'osa', 'Peaxi162Scf00067g02528' => 'pax', 'Peaxi162Scf00139g00714' => 'pax', 'Peaxi162Scf00498g00723' => 'pax', 'PGR031G2800' => 'pgr', 'PGR083G0642' => 'pgr', 'PGR119G0252' => 'pgr', 'PGR119G1256' => 'pgr', 'PGSC0003DMG400002120' => 'stu', 'PGSC0003DMG400011319' => 'stu', 'PGSC0003DMG400011393' => 'stu', 'PGSC0003DMG401002121' => 'stu', 'Phvul.001G205800' => 'pvu', 'Phvul.003G105200' => 'pvu', 'Phvul.009G247800' => 'pvu', 'Potri.005G026000' => 'ptr', 'Potri.013G017600' => 'ptr', 'Potri.014G131600' => 'ptr', 'Pp3c10_8510' => 'ppa', 'Pp3c12_25030' => 'ppa', 'Pp3c23_10040' => 'ppa', 'Pp3c24_8160' => 'ppa', 'Pp3c26_3000' => 'ppa', 'Pp3c4_3220' => 'ppa', 'PRCOL_00004081' => 'pco', 'PRCOL_00006487' => 'pco', 'Prupe.1G137200' => 'ppe', 'Prupe.6G093700' => 'ppe', 'Prupe.8G258400' => 'ppe', 'Psat1g153760' => 'psa', 'Psat2g159360' => 'psa', 'Psat3g022520' => 'psa', 'Psat3g112320' => 'psa', 'PSO170G1216' => 'pso', 'PSO210G5723' => 'pso', 'PSO339G0130' => 'pso', 'PSO384G4153' => 'pso', 'PSO591G0256' => 'pso', 'PSO832G3195' => 'pso', 'PSO832G4277' => 'pso', 'QL02p058842' => 'qlo', 'QL02p059219' => 'qlo', 'QL06p008825' => 'qlo', 'QL09p050486' => 'qlo', 'QL12p027136' => 'qlo', 'RcHm_v2.0_Chr4g0422161' => 'rch', 'RcHm_v2.0_Chr4g0422191' => 'rch', 'RcHm_v2.0_Chr6g0293561' => 'rch', 'Rhsim01G0283600' => 'rsi', 'Rhsim04G0221400' => 'rsi', 'Rhsim05G0139500' => 'rsi', 'Rhsim13G0012500' => 'rsi', 'Rhsim13G0012800' => 'rsi', 'RhsimUnG0168500' => 'rsi', 'Sabra05G0031400' => 'sbr', 'Sabra13G0016600' => 'sbr', 'Sabra13G0020600' => 'sbr', 'Sabra14G0097800' => 'sbr', 'SalBow2G2414' => 'sbo', 'SalBow3G1333' => 'sbo', 'SalBow6G1698' => 'sbo', 'SalBow7G1572' => 'sbo', 'Sc09g0005200' => 'sci', 'Sc10g0000910' => 'sci', 'Sc11g0005620' => 'sci', 'Sc11g0005640' => 'sci', 'Sed0004349' => 'sed', 'Sed0008677' => 'sed', 'Sed0019645' => 'sed', 'Sed0020155' => 'sed', 'Sed0025561' => 'sed', 'SEGI_17995' => 'sgi', 'SEGI_31251' => 'sgi', 'SEGI_31824' => 'sgi', 'SEGI_39661' => 'sgi', 'SMO111G0159' => 'smo', 'SMO144G0151' => 'smo', 'Solyc01g066840.3' => 'sly', 'Solyc04g074900.3' => 'sly', 'Solyc04g074910.3' => 'sly', 'Solyc09g074900.4' => 'sly', 'Sopen01g028440' => 'spe', 'Sopen04g029850' => 'spe', 'Sopen04g029860' => 'spe', 'Sopen09g014980' => 'spe', 'Sopen09g029720' => 'spe', 'Sp2g16650' => 'spa', 'Sp2g20860' => 'spa', 'Sp4g29690' => 'spa', 'Sp5g08510' => 'spa', 'TAR362G1163' => 'tar', 'TAR365G0358' => 'tar', 'TAR365G1088' => 'tar', 'TAR633G0725' => 'tar', 'TAR633G1201' => 'tar', 'TAR633G1634' => 'tar', 'TAR633G2480' => 'tar', 'THA.LOC104802172' => 'tha', 'THA.LOC104802798' => 'tha', 'THA.LOC104804391' => 'tha', 'THA.LOC104807233' => 'tha', 'THA.LOC104818711' => 'tha', 'THA.LOC104819542' => 'tha', 'THA.LOC104821722' => 'tha', 'Thecc.01G297200' => 'tca', 'Thecc.05G312400' => 'tca', 'Thecc.07G184400' => 'tca', 'Thecc.07G184600' => 'tca', 'Thhalv10001458m.g' => 'esa', 'Thhalv10005213m.g' => 'esa', 'Thhalv10005214m.g' => 'esa', 'Thhalv10011086m.g' => 'esa', 'TPR.G13841' => 'tpr', 'TPR.G36047' => 'tpr', 'TPR.G9626' => 'tpr', 'TWI12G0298' => 'twi', 'TWI14G0104' => 'twi', 'TWI36G1738' => 'twi', 'TWI56G0407' => 'twi', 'TWI73G0712' => 'twi', 'unitig_0.g1180' => 'ugi', 'unitig_736.g22758' => 'ugi', 'unitig_899.g14741' => 'ugi', 'vmacro02468' => 'vma', 'vmacro08147' => 'vma', 'vmacro14994' => 'vma', 'vmacro19748' => 'vma', 'Zm00001eb016600' => 'zma', 'Zm00001eb090410' => 'zma', 'Zm00001eb122900' => 'zma', 'Zm00001eb211090' => 'zma', 'Zm00001eb276520' => 'zma', 'Zm00001eb285290' => 'zma', 'Zm00001eb394850' => 'zma' ) $gf_id = 'HOM05D001496' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001496' ) $data_identifier = 'HOM05D001496' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 3, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 12, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 5, 'ghi' => (int) 16, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 16, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394850' $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